r-genomicfeatures: new package (#5811)

* r-genomicfeatures: created new package

* modified version number and added versioned dependency on r

* fixed typo

1 files changed, 58 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/r-genomicfeatures/package.py b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
new file mode 100644
index 0000000000..e3ba959de6
--- /dev/null
+++ b/var/spack/repos/builtin/packages/r-genomicfeatures/package.py
@@ -0,0 +1,58 @@
+##############################################################################
+# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the NOTICE and LICENSE files for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+
+
+class RGenomicfeatures(RPackage):
+    """A set of tools and methods for making and manipulating transcript
+       centric annotations. With these tools the user can easily download the
+       genomic locations of the transcripts, exons and cds of a given organism,
+       from either the UCSC Genome Browser or a BioMart database (more sources
+       will be supported in the future). This information is then stored in a
+       local database that keeps track of the relationship between transcripts,
+       exons, cds and genes. Flexible methods are provided for extracting the
+       desired features in a convenient format."""
+
+    homepage = "http://bioconductor.org/packages/GenomicFeatures/"
+    url      = "https://git.bioconductor.org/packages/GenomicFeatures"
+    list_url = homepage
+
+    version('1.28.5', git='https://git.bioconductor.org/packages/GenomicFeatures', commit='ba92381ae93cb1392dad5e6acfab8f6c1d744834')
+
+    depends_on('r-biocgenerics', type=('build', 'run'))
+    depends_on('r-s4vectors', type=('build', 'run'))
+    depends_on('r-iranges', type=('build', 'run'))
+    depends_on('r-genomeinfodb', type=('build', 'run'))
+    depends_on('r-genomicranges', type=('build', 'run'))
+    depends_on('r-annotationdbi', type=('build', 'run'))
+    depends_on('r-dbi', type=('build', 'run'))
+    depends_on('r-rsqlite', type=('build', 'run'))
+    depends_on('r-rcurl', type=('build', 'run'))
+    depends_on('r-xvector', type=('build', 'run'))
+    depends_on('r-biostrings', type=('build', 'run'))
+    depends_on('r-rtracklayer', type=('build', 'run'))
+    depends_on('r-biomart', type=('build', 'run'))
+    depends_on('r-biobase', type=('build', 'run'))
+    depends_on('r@3.4.0:3.4.9', when='@1.28.5')